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22143 lines
774 KiB
22143 lines
774 KiB
;;; GNU Guix --- Functional package management for GNU
|
|
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
|
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;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
|
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;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
|
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;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
|
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;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
|
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;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
|
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;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
|
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;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
|
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;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
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;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
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;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
|
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;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
|
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;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
|
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;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
|
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;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
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;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
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;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
|
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;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
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;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
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;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
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;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
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;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
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;;;
|
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;;; This file is part of GNU Guix.
|
|
;;;
|
|
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
|
;;; under the terms of the GNU General Public License as published by
|
|
;;; the Free Software Foundation; either version 3 of the License, or (at
|
|
;;; your option) any later version.
|
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;;;
|
|
;;; GNU Guix is distributed in the hope that it will be useful, but
|
|
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
;;; GNU General Public License for more details.
|
|
;;;
|
|
;;; You should have received a copy of the GNU General Public License
|
|
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
|
|
|
(define-module (gnu packages cran)
|
|
#:use-module ((guix licenses) #:prefix license:)
|
|
#:use-module (guix packages)
|
|
#:use-module (guix download)
|
|
#:use-module (guix git-download)
|
|
#:use-module (guix utils)
|
|
#:use-module (guix build-system r)
|
|
#:use-module (gnu packages algebra)
|
|
#:use-module (gnu packages autotools)
|
|
#:use-module (gnu packages base)
|
|
#:use-module (gnu packages bioinformatics)
|
|
#:use-module (gnu packages c)
|
|
#:use-module (gnu packages compression)
|
|
#:use-module (gnu packages curl)
|
|
#:use-module (gnu packages databases)
|
|
#:use-module (gnu packages fontutils)
|
|
#:use-module (gnu packages gcc)
|
|
#:use-module (gnu packages geo)
|
|
#:use-module (gnu packages ghostscript)
|
|
#:use-module (gnu packages gl)
|
|
#:use-module (gnu packages gnome)
|
|
#:use-module (gnu packages graph)
|
|
#:use-module (gnu packages gtk)
|
|
#:use-module (gnu packages haskell-xyz)
|
|
#:use-module (gnu packages icu4c)
|
|
#:use-module (gnu packages image)
|
|
#:use-module (gnu packages imagemagick)
|
|
#:use-module (gnu packages java)
|
|
#:use-module (gnu packages javascript)
|
|
#:use-module (gnu packages lisp-xyz)
|
|
#:use-module (gnu packages machine-learning)
|
|
#:use-module (gnu packages maths)
|
|
#:use-module (gnu packages mpi)
|
|
#:use-module (gnu packages multiprecision)
|
|
#:use-module (gnu packages networking)
|
|
#:use-module (gnu packages node)
|
|
#:use-module (gnu packages pcre)
|
|
#:use-module (gnu packages perl)
|
|
#:use-module (gnu packages pkg-config)
|
|
#:use-module (gnu packages pulseaudio) ;libsndfile
|
|
#:use-module (gnu packages python)
|
|
#:use-module (gnu packages python-xyz)
|
|
#:use-module (gnu packages statistics)
|
|
#:use-module (gnu packages tcl)
|
|
#:use-module (gnu packages tls)
|
|
#:use-module (gnu packages web)
|
|
#:use-module (gnu packages xorg))
|
|
|
|
(define-public r-bezier
|
|
(package
|
|
(name "r-bezier")
|
|
(version "1.1.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bezier" version))
|
|
(sha256
|
|
(base32
|
|
"1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/bezier/")
|
|
(synopsis "Bezier curve and spline toolkit")
|
|
(description
|
|
"This package is a toolkit for working with Bezier curves and splines.
|
|
The package provides functions for point generation, arc length estimation,
|
|
degree elevation and curve fitting.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-v8
|
|
(package
|
|
(name "r-v8")
|
|
(version "3.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "V8" version))
|
|
(sha256
|
|
(base32
|
|
"0z0dwa538lkggawiwrlplz698xznzlgv9fwhdslm7g7gdxyf0xgm"))))
|
|
(properties `((upstream-name . "V8")))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'find-v8
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(substitute* "configure"
|
|
(("^PKG_LIBS=.*")
|
|
(string-append "PKG_LIBS="
|
|
(assoc-ref inputs "node")
|
|
"/lib/libnode.so.64\n")))
|
|
(setenv "INCLUDE_DIR"
|
|
(string-append
|
|
(assoc-ref inputs "node")
|
|
"/include/node"))
|
|
(setenv "LIB_DIR"
|
|
(string-append
|
|
(assoc-ref inputs "node") "/lib"))
|
|
#t)))))
|
|
(inputs
|
|
`(("node" ,libnode)))
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://jeroen.cran.dev/V8")
|
|
(synopsis "Embedded JavaScript and WebAssembly engine for R")
|
|
(description
|
|
"This package provides an R interface to V8: Google's JavaScript and
|
|
WebAssembly engine.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-dot
|
|
(package
|
|
(name "r-dot")
|
|
(version "0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "DOT" version))
|
|
(sha256
|
|
(base32
|
|
"0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
|
|
(properties `((upstream-name . "DOT")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-v8" ,r-v8)))
|
|
(home-page "http://haghish.com/dot")
|
|
(synopsis "Render and Export DOT Graphs in R")
|
|
(description
|
|
"This package provides tools to render DOT diagram markup language in R
|
|
and also provides the possibility to export the graphs in PostScript and
|
|
SVG (Scalable Vector Graphics) formats. In addition, it supports literate
|
|
programming packages such as @code{knitr} and @code{rmarkdown}.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-clipr
|
|
(package
|
|
(name "r-clipr")
|
|
(version "0.7.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "clipr" version))
|
|
(sha256
|
|
(base32
|
|
"1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/mdlincoln/clipr")
|
|
(synopsis "Read and write from the system clipboard")
|
|
(description
|
|
"This package provides simple utility functions to read from and write to
|
|
the system clipboards.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-ggpmisc
|
|
(package
|
|
(name "r-ggpmisc")
|
|
(version "0.3.5")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggpmisc" version))
|
|
(sha256
|
|
(base32
|
|
"0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-broom" ,r-broom)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-lubridate" ,r-lubridate)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-mass" ,r-mass)
|
|
("r-plyr" ,r-plyr)
|
|
("r-polynom" ,r-polynom)
|
|
("r-rlang" ,r-rlang)
|
|
("r-scales" ,r-scales)
|
|
("r-splus2r" ,r-splus2r)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tibble" ,r-tibble)
|
|
("r-xts" ,r-xts)
|
|
("r-zoo" ,r-zoo)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://www.r4photobiology.info/")
|
|
(synopsis "Miscellaneous Extensions to @code{ggplot2}")
|
|
(description "This package provides extensions to @code{ggplot2},
|
|
respecting the grammar of its graphics paradigm.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-gprofiler
|
|
(package
|
|
(name "r-gprofiler")
|
|
(version "0.7.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gProfileR" version))
|
|
(sha256
|
|
(base32
|
|
"1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
|
|
(properties `((upstream-name . "gProfileR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-plyr" ,r-plyr)
|
|
("r-rcurl" ,r-rcurl)))
|
|
(home-page "https://cran.r-project.org/web/packages/gProfileR/")
|
|
(synopsis "Interface to the g:Profiler toolkit")
|
|
(description
|
|
"This package provides tools for functional enrichment analysis,
|
|
gene identifier conversion and mapping homologous genes across related
|
|
organisms via the @code{g:Profiler} toolkit.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-gprofiler2
|
|
(package
|
|
(name "r-gprofiler2")
|
|
(version "0.1.9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gprofiler2" version))
|
|
(sha256
|
|
(base32
|
|
"112hmmvdwg8xz90w1bsbzc55y4xi9jj4dqy0q4bsgp49x58r92rb"))))
|
|
(properties `((upstream-name . "gprofiler2")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-crosstalk" ,r-crosstalk)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-plotly" ,r-plotly)
|
|
("r-rcurl" ,r-rcurl)
|
|
("r-tidyr" ,r-tidyr)
|
|
("r-viridislite" ,r-viridislite)))
|
|
(native-inputs `(("r-knitr" ,r-knitr)))
|
|
(home-page "https://cran.r-project.org/web/packages/gprofiler2/")
|
|
(synopsis "Interface to the g:Profiler toolset")
|
|
(description
|
|
"This package provides a toolset for functional enrichment analysis and
|
|
visualization, gene/protein/SNP identifier conversion and mapping orthologous
|
|
genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
|
|
The main tools are:
|
|
|
|
@enumerate
|
|
@item @code{g:GOSt}, functional enrichment analysis and visualization of gene
|
|
lists;
|
|
@item @code{g:Convert}, gene/protein/transcript identifier conversion across
|
|
various namespaces;
|
|
@item @code{g:Orth}, orthology search across species;
|
|
@item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
|
|
genes and variant effects.
|
|
@end enumerate
|
|
|
|
This package is an R interface corresponding to the 2019 update of
|
|
@code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
|
|
higher.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-oenb
|
|
(package
|
|
(name "r-oenb")
|
|
(version "0.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "oenb" version))
|
|
(sha256
|
|
(base32
|
|
"1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
|
|
(properties `((upstream-name . "oenb")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-xml" ,r-xml)))
|
|
(native-inputs `(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/franzmohr/oenb")
|
|
(synopsis "Tools for the OeNB Data Web Service")
|
|
(description
|
|
"Tools to access data from the data web service of the
|
|
@acronym{OeNB, Oesterreichische Nationalbank},
|
|
@url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-scales
|
|
(package
|
|
(name "r-scales")
|
|
(version "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "scales" version))
|
|
(sha256
|
|
(base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-farver" ,r-farver)
|
|
("r-labeling" ,r-labeling)
|
|
("r-lifecycle" ,r-lifecycle)
|
|
("r-munsell" ,r-munsell)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-r6" ,r-r6)
|
|
("r-viridislite" ,r-viridislite)))
|
|
(home-page "https://github.com/hadley/scales")
|
|
(synopsis "Scale functions for visualization")
|
|
(description
|
|
"This package provides graphical scales that map data to aesthetics, and
|
|
provides methods for automatically determining breaks and labels for axes and
|
|
legends.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-pheatmap
|
|
(package
|
|
(name "r-pheatmap")
|
|
(version "1.0.12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pheatmap" version))
|
|
(sha256
|
|
(base32
|
|
"1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-gtable" ,r-gtable)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-scales" ,r-scales)))
|
|
(home-page "https://cran.r-project.org/web/packages/pheatmap")
|
|
(synopsis "Pretty heatmaps")
|
|
(description
|
|
"This package provides an implementation of heatmaps that offers more
|
|
control over dimensions and appearance.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ecp
|
|
(package
|
|
(name "r-ecp")
|
|
(version "3.1.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ecp" version))
|
|
(sha256
|
|
(base32
|
|
"11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/ecp/")
|
|
(synopsis "Multiple change-point analysis of multivariate data")
|
|
(description
|
|
"This package implements various procedures for finding multiple
|
|
change-points. Two methods make use of dynamic programming and pruning, with
|
|
no distributional assumptions other than the existence of certain absolute
|
|
moments in one method. Hierarchical and exact search methods are included.
|
|
All methods return the set of estimated change-points as well as other summary
|
|
information.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ellipsis
|
|
(package
|
|
(name "r-ellipsis")
|
|
(version "0.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ellipsis" version))
|
|
(sha256
|
|
(base32
|
|
"1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rlang" ,r-rlang)))
|
|
(home-page "https://github.com/hadley/ellipsis")
|
|
(synopsis "Tools for working with additional arguments")
|
|
(description
|
|
"In S3 generics, it's useful to take @code{...} so that methods can have
|
|
additional arguments. But this flexibility comes at a cost: misspelled
|
|
arguments will be silently ignored. The @code{ellipsis} package is an
|
|
experiment that allows a generic to warn if any arguments passed in @code{...}
|
|
are not used.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-grr
|
|
(package
|
|
(name "r-grr")
|
|
(version "0.9.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "grr" version))
|
|
(sha256
|
|
(base32
|
|
"0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/grr")
|
|
(synopsis "Alternative implementations of base R functions")
|
|
(description
|
|
"This package provides alternative implementations of some base R
|
|
functions, including @code{sort}, @code{order}, and @code{match}. The
|
|
functions are simplified but can be faster or have other advantages.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-matrix-utils
|
|
(package
|
|
(name "r-matrix-utils")
|
|
(version "0.9.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Matrix.utils" version))
|
|
(sha256
|
|
(base32
|
|
"0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
|
|
(properties `((upstream-name . "Matrix.utils")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-grr" ,r-grr)
|
|
("r-matrix" ,r-matrix)))
|
|
(home-page "https://github.com/cvarrichio/Matrix.utils")
|
|
(synopsis
|
|
"Data.frame-Like Operations on Sparse and Dense Matrix Objects")
|
|
(description
|
|
"This package implements data manipulation methods such as @code{cast},
|
|
@code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
|
|
objects.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-sys
|
|
(package
|
|
(name "r-sys")
|
|
(version "3.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sys" version))
|
|
(sha256
|
|
(base32
|
|
"14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/jeroen/sys")
|
|
(synopsis "Powerful and reliable tools for running system commands in R")
|
|
(description
|
|
"This package provides drop-in replacements for the base @code{system2()}
|
|
function with fine control and consistent behavior across platforms. It
|
|
supports clean interruption, timeout, background tasks, and streaming STDIN /
|
|
STDOUT / STDERR over binary or text connections. The package also provides
|
|
functions for evaluating expressions inside a temporary fork. Such
|
|
evaluations have no side effects on the main R process, and support reliable
|
|
interrupts and timeouts. This provides the basis for a sandboxing
|
|
mechanism.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-askpass
|
|
(package
|
|
(name "r-askpass")
|
|
(version "1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "askpass" version))
|
|
(sha256
|
|
(base32
|
|
"07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-sys" ,r-sys)))
|
|
(home-page "https://github.com/jeroen/askpass")
|
|
(synopsis "Safe password entry for R")
|
|
(description
|
|
"This package provides cross-platform utilities for prompting the user
|
|
for credentials or a passphrase, for example to authenticate with a server or
|
|
read a protected key.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-vegan
|
|
(package
|
|
(name "r-vegan")
|
|
(version "2.5-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "vegan" version))
|
|
(sha256
|
|
(base32
|
|
"0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(propagated-inputs
|
|
`(("r-cluster" ,r-cluster)
|
|
("r-knitr" ,r-knitr) ; needed for vignettes
|
|
("r-lattice" ,r-lattice)
|
|
("r-mass" ,r-mass)
|
|
("r-mgcv" ,r-mgcv)
|
|
("r-permute" ,r-permute)))
|
|
(home-page "https://cran.r-project.org/web/packages/vegan")
|
|
(synopsis "Functions for community ecology")
|
|
(description
|
|
"The vegan package provides tools for descriptive community ecology. It
|
|
has most basic functions of diversity analysis, community ordination and
|
|
dissimilarity analysis. Most of its multivariate tools can be used for other
|
|
data types as well.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-tidyverse
|
|
(package
|
|
(name "r-tidyverse")
|
|
(version "1.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tidyverse" version))
|
|
(sha256
|
|
(base32
|
|
"02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-broom" ,r-broom)
|
|
("r-cli" ,r-cli)
|
|
("r-crayon" ,r-crayon)
|
|
("r-dbplyr" ,r-dbplyr)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-forcats" ,r-forcats)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-haven" ,r-haven)
|
|
("r-hms" ,r-hms)
|
|
("r-httr" ,r-httr)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-lubridate" ,r-lubridate)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-modelr" ,r-modelr)
|
|
("r-pillar" ,r-pillar)
|
|
("r-purrr" ,r-purrr)
|
|
("r-readr" ,r-readr)
|
|
("r-readxl" ,r-readxl)
|
|
("r-reprex" ,r-reprex)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-rvest" ,r-rvest)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)
|
|
("r-xml2" ,r-xml2)))
|
|
(home-page "https://tidyverse.tidyverse.org")
|
|
(synopsis "Install and load packages from the \"Tidyverse\"")
|
|
(description
|
|
"The @code{tidyverse} is a set of packages that work in harmony because
|
|
they share common data representations and API design. This package is
|
|
designed to make it easy to install and load multiple tidyverse packages in a
|
|
single step.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-rvest
|
|
(package
|
|
(name "r-rvest")
|
|
(version "0.3.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rvest" version))
|
|
(sha256
|
|
(base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-httr" ,r-httr)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-selectr" ,r-selectr)
|
|
("r-xml2" ,r-xml2)))
|
|
(home-page "https://github.com/hadley/rvest")
|
|
(synopsis "Simple web scraping for R")
|
|
(description
|
|
"@code{r-rvest} helps you scrape information from web pages. It is
|
|
designed to work with @code{magrittr} to make it easy to express common web
|
|
scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-selectr
|
|
(package
|
|
(name "r-selectr")
|
|
(version "0.4-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "selectr" version))
|
|
(sha256
|
|
(base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-stringr" ,r-stringr)
|
|
("r-r6" ,r-r6)))
|
|
(home-page "https://sjp.co.nz/projects/selectr/")
|
|
(synopsis "Translate CSS selectors to XPath expressions")
|
|
(description
|
|
"@code{r-selectr} translates a CSS3 selector into an equivalent XPath
|
|
expression. This allows you to use CSS selectors when working with the XML
|
|
package as it can only evaluate XPath expressions. Also provided are
|
|
convenience functions useful for using CSS selectors on XML nodes. This
|
|
package is a port of the Python package @code{cssselect}.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-reprex
|
|
(package
|
|
(name "r-reprex")
|
|
(version "0.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "reprex" version))
|
|
(sha256
|
|
(base32
|
|
"0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-callr" ,r-callr)
|
|
("r-clipr" ,r-clipr)
|
|
("r-fs" ,r-fs)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rmarkdown" ,r-rmarkdown)
|
|
("r-whisker" ,r-whisker)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/tidyverse/reprex")
|
|
(synopsis "Prepare reproducible R code examples for sharing")
|
|
(description
|
|
"This package provides a convenience wrapper that uses the
|
|
@code{rmarkdown} package to render small snippets of code to target formats
|
|
that include both code and output. The goal is to encourage the sharing of
|
|
small, reproducible, and runnable examples on code-oriented websites or email.
|
|
@code{reprex} also extracts clean, runnable R code from various common formats,
|
|
such as copy/paste from an R session.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-reordercluster
|
|
(package
|
|
(name "r-reordercluster")
|
|
(version "1.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ReorderCluster" version))
|
|
(sha256
|
|
(base32
|
|
"0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-gplots" ,r-gplots)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/ReorderCluster")
|
|
(synopsis "Reordering the dendrogram according to the class labels")
|
|
(description "This package provides tools for performing the leaf reordering
|
|
for the dendrogram that preserves the hierarchical clustering result and at the
|
|
same time tries to group instances from the same class together.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-callr
|
|
(package
|
|
(name "r-callr")
|
|
(version "3.4.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "callr" version))
|
|
(sha256
|
|
(base32
|
|
"1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-r6" ,r-r6)
|
|
("r-processx" ,r-processx)))
|
|
(home-page "https://github.com/r-lib/callr#readme")
|
|
(synopsis "Call R from R")
|
|
(description
|
|
"It is sometimes useful to perform a computation in a separate R process,
|
|
without affecting the current R process at all. This package does exactly
|
|
that.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-readxl
|
|
(package
|
|
(name "r-readxl")
|
|
(version "1.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "readxl" version))
|
|
(sha256
|
|
(base32
|
|
"15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cellranger" ,r-cellranger)
|
|
("r-progress" ,r-progress)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://readxl.tidyverse.org")
|
|
(synopsis "Read Excel files")
|
|
(description
|
|
"This package lets you import Excel files into R. It supports
|
|
@file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
|
|
the embedded @code{RapidXML} C++ library.")
|
|
;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
|
|
;; 'rapidxml' which is Boost.
|
|
(license (list license:gpl3 license:bsd-2 license:boost1.0))))
|
|
|
|
(define-public r-modelr
|
|
(package
|
|
(name "r-modelr")
|
|
(version "0.1.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "modelr" version))
|
|
(sha256
|
|
(base32
|
|
"1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-broom" ,r-broom)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)
|
|
("r-tidyselect" ,r-tidyselect)
|
|
("r-vctrs" ,r-vctrs)))
|
|
(home-page "https://github.com/tidyverse/modelr")
|
|
(synopsis "Helper functions for modelling in pipelines")
|
|
(description
|
|
"Functions for modelling that help you seamlessly integrate modelling
|
|
into a pipeline of data manipulation and visualisation.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-httpuv
|
|
(package
|
|
(name "r-httpuv")
|
|
(version "1.5.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "httpuv" version))
|
|
(sha256
|
|
(base32
|
|
"066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bh" ,r-bh)
|
|
("r-later" ,r-later)
|
|
("r-promises" ,r-promises)
|
|
("r-r6" ,r-r6)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/rstudio/httpuv")
|
|
(synopsis "HTTP and WebSocket server library for R")
|
|
(description
|
|
"The httpuv package provides low-level socket and protocol support for
|
|
handling HTTP and WebSocket requests directly from within R. It is primarily
|
|
intended as a building block for other packages, rather than making it
|
|
particularly easy to create complete web applications using httpuv alone.")
|
|
;; This package includes third-party code that was originally released
|
|
;; under various non-copyleft licenses. Full licensing information can be
|
|
;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-jsonlite
|
|
(package
|
|
(name "r-jsonlite")
|
|
(version "1.6.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "jsonlite" version))
|
|
(sha256
|
|
(base32
|
|
"0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://arxiv.org/abs/1403.2805")
|
|
(synopsis "Robust, high performance JSON parser and generator for R")
|
|
(description
|
|
"The jsonlite package provides a fast JSON parser and generator optimized
|
|
for statistical data and the web. It offers flexible, robust, high
|
|
performance tools for working with JSON in R and is particularly powerful for
|
|
building pipelines and interacting with a web API. In addition to converting
|
|
JSON data from/to R objects, jsonlite contains functions to stream, validate,
|
|
and prettify JSON data. The unit tests included with the package verify that
|
|
all edge cases are encoded and decoded consistently for use with dynamic data
|
|
in systems and applications.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-servr
|
|
(package
|
|
(name "r-servr")
|
|
(version "0.17")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "servr" version))
|
|
(sha256
|
|
(base32
|
|
"0lxkjr7mwdk96cdpx66j92nn4w2vkgn2j2bbg7kd4238jsk9srs7"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-httpuv" ,r-httpuv)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-mime" ,r-mime)
|
|
("r-xfun" ,r-xfun)))
|
|
(home-page "https://github.com/yihui/servr")
|
|
(synopsis "Simple HTTP server to serve static files or dynamic documents")
|
|
(description
|
|
"Servr provides an HTTP server in R to serve static files, or dynamic
|
|
documents that can be converted to HTML files (e.g., R Markdown) under a given
|
|
directory.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-htmltools
|
|
(package
|
|
(name "r-htmltools")
|
|
(version "0.5.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "htmltools" version))
|
|
(sha256
|
|
(base32
|
|
"07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-digest" ,r-digest)
|
|
("r-rlang" ,r-rlang)))
|
|
(home-page "https://cran.r-project.org/web/packages/htmltools")
|
|
(synopsis "R tools for HTML")
|
|
(description
|
|
"This package provides tools for HTML generation and output in R.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-htmlwidgets
|
|
(package
|
|
(name "r-htmlwidgets")
|
|
(version "1.5.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "htmlwidgets" version))
|
|
(sha256
|
|
(base32
|
|
"10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-yaml" ,r-yaml)))
|
|
(home-page "https://github.com/ramnathv/htmlwidgets")
|
|
(synopsis "HTML Widgets for R")
|
|
(description
|
|
"HTML widgets is a framework for creating HTML widgets that render in
|
|
various contexts including the R console, R Markdown documents, and Shiny web
|
|
applications.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-htmltable
|
|
(package
|
|
(name "r-htmltable")
|
|
(version "2.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "htmlTable" version))
|
|
(sha256
|
|
(base32
|
|
"1a1al4kld7lrapc2i086crr78kbgrskahs221iy9v77x0nhin2q3"))))
|
|
(properties `((upstream-name . "htmlTable")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-checkmate" ,r-checkmate)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-knitr" ,r-knitr)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-stringr" ,r-stringr)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "http://gforge.se/packages/")
|
|
(synopsis "Advanced tables for Markdown/HTML")
|
|
(description
|
|
"This package provides functions to build tables with advanced layout
|
|
elements such as row spanners, column spanners, table spanners, zebra
|
|
striping, and more. While allowing advanced layout, the underlying
|
|
CSS-structure is simple in order to maximize compatibility with word
|
|
processors such as LibreOffice. The package also contains a few text
|
|
formatting functions that help outputting text compatible with HTML or
|
|
LaTeX.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-curl
|
|
(package
|
|
(name "r-curl")
|
|
(version "4.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "curl" version))
|
|
(sha256
|
|
(base32
|
|
"1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
;; The environment variable CURL_CA_BUNDLE is only respected when
|
|
;; running Windows, so we disable the platform checks.
|
|
;; This can be removed once the libcurl has been patched.
|
|
(add-after 'unpack 'allow-CURL_CA_BUNDLE
|
|
(lambda _
|
|
(substitute* "R/onload.R"
|
|
(("if \\(!grepl\\(\"mingw\".*")
|
|
"if (FALSE)\n"))
|
|
(substitute* "src/handle.c"
|
|
(("/\\* Only set" m)
|
|
(string-append "\
|
|
const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
|
|
if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
|
|
" m)))
|
|
#t)))))
|
|
(inputs
|
|
`(("libcurl" ,curl)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "https://github.com/jeroenooms/curl")
|
|
(synopsis "HTTP client for R")
|
|
(description
|
|
"The @code{curl()} and @code{curl_download()} functions provide highly
|
|
configurable drop-in replacements for base @code{url()} and
|
|
@code{download.file()} with better performance, support for encryption, gzip
|
|
compression, authentication, and other @code{libcurl} goodies. The core of
|
|
the package implements a framework for performing fully customized requests
|
|
where data can be processed either in memory, on disk, or streaming via the
|
|
callback or connection interfaces.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-hwriter
|
|
(package
|
|
(name "r-hwriter")
|
|
(version "1.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "hwriter" version))
|
|
(sha256
|
|
(base32
|
|
"0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/hwriter")
|
|
(synopsis "Output R objects in HTML format")
|
|
(description
|
|
"This package provides easy-to-use and versatile functions to output R
|
|
objects in HTML format.")
|
|
(license license:lgpl2.1+)))
|
|
|
|
(define-public r-rjson
|
|
(package
|
|
(name "r-rjson")
|
|
(version "0.2.20")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rjson" version))
|
|
(sha256
|
|
(base32
|
|
"0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/rjson")
|
|
(synopsis "JSON library for R")
|
|
(description
|
|
"This package provides functions to convert R objects into JSON objects
|
|
and vice-versa.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-fastmap
|
|
(package
|
|
(name "r-fastmap")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fastmap" version))
|
|
(sha256
|
|
(base32
|
|
"1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
|
|
(properties `((upstream-name . "fastmap")))
|
|
(build-system r-build-system)
|
|
(home-page "https://r-lib.github.io/fastmap/")
|
|
(synopsis "Fast implementation of a key-value store")
|
|
(description
|
|
"This package provides a fast implementation of a key-value store.
|
|
Environments are commonly used as key-value stores, but every time a new key
|
|
is used, it is added to R's global symbol table, causing a small amount of
|
|
memory leakage. This can be problematic in cases where many different keys
|
|
are used. Fastmap avoids this memory leak issue by implementing the map using
|
|
data structures in C++.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-shiny
|
|
(package
|
|
(name "r-shiny")
|
|
(version "1.4.0.2")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/rstudio/shiny.git")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:modules ((guix build r-build-system)
|
|
(guix build minify-build-system)
|
|
(guix build utils)
|
|
(ice-9 match))
|
|
#:imported-modules (,@%r-build-system-modules
|
|
(guix build minify-build-system))
|
|
#:phases
|
|
(modify-phases (@ (guix build r-build-system) %standard-phases)
|
|
(add-after 'unpack 'replace-bundled-minified-JavaScript
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(let ((replace-file (lambda (old new)
|
|
(format #t "replacing ~a with ~a\n" old new)
|
|
(delete-file old)
|
|
(symlink new old))))
|
|
;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
|
|
;; contain just data. They are not minified code, so we don't
|
|
;; replace them.
|
|
(with-directory-excursion "inst/www/shared"
|
|
(replace-file "bootstrap/shim/respond.min.js"
|
|
(string-append (assoc-ref inputs "js-respond")
|
|
"/share/javascript/respond.min.js"))
|
|
(replace-file "bootstrap/shim/html5shiv.min.js"
|
|
(string-append (assoc-ref inputs "js-html5shiv")
|
|
"/share/javascript/html5shiv.min.js"))
|
|
(replace-file "json2-min.js"
|
|
(string-append (assoc-ref inputs "js-json2")
|
|
"/share/javascript/json2-min.js"))
|
|
(replace-file "strftime/strftime-min.js"
|
|
(string-append (assoc-ref inputs "js-strftime")
|
|
"/share/javascript/strftime.min.js"))
|
|
(replace-file "highlight/highlight.pack.js"
|
|
(string-append (assoc-ref inputs "js-highlight")
|
|
"/share/javascript/highlight.min.js"))
|
|
(replace-file "datatables/js/jquery.dataTables.min.js"
|
|
(string-append (assoc-ref inputs "js-datatables")
|
|
"/share/javascript/jquery.dataTables.min.js"))
|
|
(replace-file "selectize/js/selectize.min.js"
|
|
(string-append (assoc-ref inputs "js-selectize")
|
|
"/share/javascript/selectize.min.js"))
|
|
(replace-file "selectize/js/es5-shim.min.js"
|
|
(string-append (assoc-ref inputs "js-es5-shim")
|
|
"/share/javascript/es5-shim.min.js"))
|
|
(for-each (match-lambda
|
|
((source . target)
|
|
(delete-file target)
|
|
(minify source #:target target)))
|
|
'(("jqueryui/jquery-ui.js" .
|
|
"jqueryui/jquery-ui.min.js")
|
|
("datepicker/js/bootstrap-datepicker.js" .
|
|
"datepicker/js/bootstrap-datepicker.min.js")
|
|
("ionrangeslider/js/ion.rangeSlider.js" .
|
|
"ionrangeslider/js/ion.rangeSlider.min.js")
|
|
("bootstrap/js/bootstrap.js" .
|
|
"bootstrap/js/bootstrap.min.js")
|
|
("shiny.js" .
|
|
"shiny.min.js")
|
|
("jquery.js" .
|
|
"jquery.min.js")
|
|
("legacy/jquery.js" .
|
|
"legacy/jquery.min.js")
|
|
("showdown/src/showdown.js" .
|
|
"showdown/compressed/showdown.js")))))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("r-crayon" ,r-crayon)
|
|
("r-digest" ,r-digest)
|
|
("r-fastmap" ,r-fastmap)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-httpuv" ,r-httpuv)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-later" ,r-later)
|
|
("r-mime" ,r-mime)
|
|
("r-promises" ,r-promises)
|
|
("r-r6" ,r-r6)
|
|
("r-rlang" ,r-rlang)
|
|
("r-sourcetools" ,r-sourcetools)
|
|
("r-withr" ,r-withr)
|
|
("r-xtable" ,r-xtable)))
|
|
(inputs
|
|
`(("js-datatables" ,js-datatables)
|
|
("js-html5shiv" ,js-html5shiv)
|
|
("js-json2" ,js-json2)
|
|
("js-respond" ,js-respond)
|
|
("js-selectize" ,js-selectize)
|
|
("js-strftime" ,js-strftime)
|
|
("js-highlight" ,js-highlight)
|
|
("js-es5-shim" ,js-es5-shim)))
|
|
(native-inputs
|
|
`(("uglify-js" ,uglify-js)
|
|
("gfortran" ,gfortran)))
|
|
(home-page "http://shiny.rstudio.com")
|
|
(synopsis "Easy interactive web applications with R")
|
|
(description
|
|
"Makes it incredibly easy to build interactive web applications
|
|
with R. Automatic \"reactive\" binding between inputs and outputs and
|
|
extensive prebuilt widgets make it possible to build beautiful,
|
|
responsive, and powerful applications with minimal effort.")
|
|
(license license:artistic2.0)))
|
|
|
|
;; This package includes minified JavaScript files. When upgrading please
|
|
;; check that there are no new minified JavaScript files.
|
|
(define-public r-shinytree
|
|
(package
|
|
(name "r-shinytree")
|
|
(version "0.2.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shinyTree" version))
|
|
(sha256
|
|
(base32
|
|
"0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(begin
|
|
;; Delete minified JavaScript
|
|
(for-each delete-file
|
|
'("inst/www/jsTree-3.3.7/libs/require.js"
|
|
"inst/www/jsTree-3.3.7/libs/jquery.js"
|
|
"inst/www/jsTree-3.3.7/jstree.min.js"))
|
|
#t))))
|
|
(properties `((upstream-name . "shinyTree")))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:modules ((guix build utils)
|
|
(guix build r-build-system)
|
|
(srfi srfi-1)
|
|
(ice-9 popen))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'replace-minified-javascript
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(with-directory-excursion "inst/www/jsTree-3.3.7/"
|
|
(symlink (string-append (assoc-ref inputs "js-requirejs")
|
|
"/share/javascript/require.min.js")
|
|
"libs/require.js")
|
|
(call-with-values
|
|
(lambda ()
|
|
(unzip2
|
|
`((,(assoc-ref inputs "js-jquery")
|
|
"libs/jquery.js")
|
|
("jstree.js"
|
|
"jstree.min.js"))))
|
|
(lambda (sources targets)
|
|
(for-each (lambda (source target)
|
|
(format #t "Processing ~a --> ~a~%"
|
|
source target)
|
|
(let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
|
|
(call-with-output-file target
|
|
(lambda (port)
|
|
(dump-port minified port)))))
|
|
sources targets))))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-promises" ,r-promises)
|
|
("r-shiny" ,r-shiny)
|
|
("r-stringr" ,r-stringr)))
|
|
(inputs
|
|
`(("js-requirejs" ,js-requirejs)))
|
|
(native-inputs
|
|
`(("uglify-js" ,uglify-js)
|
|
("js-jquery"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://code.jquery.com/jquery-3.3.1.js")
|
|
(sha256
|
|
(base32
|
|
"1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
|
|
(home-page "https://cran.r-project.org/web/packages/shinyTree/")
|
|
(synopsis "jsTree bindings for Shiny")
|
|
(description
|
|
"This package exposes R bindings to jsTree, a JavaScript library that
|
|
supports interactive trees, to enable rich, editable trees in Shiny.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-shinydashboard
|
|
(package
|
|
(name "r-shinydashboard")
|
|
(version "0.7.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shinydashboard" version))
|
|
(sha256
|
|
(base32
|
|
"0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
|
|
(build-system r-build-system)
|
|
;; The directory inst/AdminLTE/ contains a minified JavaScript file.
|
|
;; Regenerate it from the included sources.
|
|
(arguments
|
|
`(#:modules ((guix build utils)
|
|
(guix build r-build-system)
|
|
(ice-9 popen))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'generate-minified-javascript
|
|
(lambda _
|
|
(with-directory-excursion "inst/AdminLTE"
|
|
(delete-file "app.min.js")
|
|
(let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
|
|
(call-with-output-file "app.min.js"
|
|
(lambda (port)
|
|
(dump-port minified port))))))))))
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-promises" ,r-promises)
|
|
("r-shiny" ,r-shiny)))
|
|
(native-inputs
|
|
`(("uglify-js" ,uglify-js)))
|
|
(home-page "https://rstudio.github.io/shinydashboard/")
|
|
(synopsis "Create dashboards with shiny")
|
|
(description "This package provides an extension to the Shiny web
|
|
application framework for R, making it easy to create attractive dashboards.")
|
|
;; This package includes software that was released under the Expat
|
|
;; license, but the whole package is released under GPL version 2 or
|
|
;; later.
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-shinyfiles
|
|
(package
|
|
(name "r-shinyfiles")
|
|
(version "0.8.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shinyFiles" version))
|
|
(sha256
|
|
(base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
|
|
(properties `((upstream-name . "shinyFiles")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-fs" ,r-fs)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-shiny" ,r-shiny)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://github.com/thomasp85/shinyFiles")
|
|
(synopsis "Server-side file system viewer for Shiny")
|
|
(description
|
|
"This package provides functionality for client-side navigation of the
|
|
server side file system in shiny apps. In case the app is running locally
|
|
this gives the user direct access to the file system without the need to
|
|
\"download\" files to a temporary location. Both file and folder selection as
|
|
well as file saving is available.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-shinythemes
|
|
(package
|
|
(name "r-shinythemes")
|
|
(version "1.1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shinythemes" version))
|
|
(sha256
|
|
(base32
|
|
"12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
|
|
(properties `((upstream-name . "shinythemes")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-shiny" ,r-shiny)))
|
|
(home-page "https://rstudio.github.io/shinythemes/")
|
|
(synopsis "Themes for Shiny")
|
|
(description
|
|
"This package provides themes for use with Shiny. It includes several
|
|
Bootstrap themes, which are packaged for use with Shiny applications.")
|
|
;; The package is released under version 3 of the GPL, but it includes
|
|
;; source files that are covered by the Expat license. It also includes
|
|
;; fonts under SIL or the ASL.
|
|
(license (list license:gpl3 license:expat
|
|
license:silofl1.1 license:asl2.0))))
|
|
|
|
;; The package sources include minified variants of d3.js and non-minified
|
|
;; source code of d3-jetpack.
|
|
(define-public r-d3r
|
|
(package
|
|
(name "r-d3r")
|
|
(version "0.9.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "d3r" version))
|
|
(sha256
|
|
(base32
|
|
"0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:modules ((guix build utils)
|
|
(guix build r-build-system)
|
|
(srfi srfi-1)
|
|
(ice-9 popen))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'process-javascript
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(with-directory-excursion "inst/www/d3/"
|
|
(call-with-values
|
|
(lambda ()
|
|
(unzip2
|
|
`((,(assoc-ref inputs "d3.v3.js")
|
|
"v3/dist/d3.min.js")
|
|
(,(assoc-ref inputs "d3.v4.js")
|
|
"v4/dist/d3.min.js")
|
|
(,(assoc-ref inputs "d3.v5.js")
|
|
"v5/dist/d3.min.js"))))
|
|
(lambda (sources targets)
|
|
(for-each (lambda (source target)
|
|
(format #t "Processing ~a --> ~a~%"
|
|
source target)
|
|
(delete-file target)
|
|
(let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
|
|
(call-with-output-file target
|
|
(lambda (port)
|
|
(dump-port minified port)))))
|
|
sources targets))))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(native-inputs
|
|
`(("uglify-js" ,uglify-js)
|
|
("d3.v3.js"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://d3js.org/d3.v3.js")
|
|
(sha256
|
|
(base32
|
|
"1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
|
|
("d3.v4.js"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://d3js.org/d3.v4.js")
|
|
(sha256
|
|
(base32
|
|
"0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
|
|
("d3.v5.js"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://d3js.org/d3.v5.js")
|
|
(sha256
|
|
(base32
|
|
"0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
|
|
(home-page "https://github.com/timelyportfolio/d3r")
|
|
(synopsis "d3.js utilities for R")
|
|
(description
|
|
"This package provides a suite of functions to help ease the use of the
|
|
d3.js visualization library in R. These helpers include
|
|
@code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
|
|
tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
|
|
R objects into the JSON format that the d3.js library expects.")
|
|
(license license:bsd-3)))
|
|
|
|
;; We use the latest commit here because the last release was in 2016 while
|
|
;; the latest commit was in 2018.
|
|
(define-public r-sankeyd3
|
|
(let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
|
|
(revision "1"))
|
|
(package
|
|
(name "r-sankeyd3")
|
|
(version (git-version "0.3.2" revision commit))
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/fbreitwieser/sankeyD3.git")
|
|
(commit commit)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-d3r" ,r-d3r)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-shiny" ,r-shiny)
|
|
("r-magrittr" ,r-magrittr)))
|
|
(home-page "https://github.com/fbreitwieser/sankeyD3")
|
|
(synopsis "Sankey network graphs from R")
|
|
(description
|
|
"This package provides an R library to generate Sankey network graphs
|
|
in R and Shiny via the D3 visualization library.")
|
|
;; The R code is licensed under GPLv3+. It includes the non-minified
|
|
;; JavaScript source code of d3-sankey, which is released under the
|
|
;; 3-clause BSD license.
|
|
(license (list license:gpl3+ license:bsd-3)))))
|
|
|
|
(define-public r-crosstalk
|
|
(package
|
|
(name "r-crosstalk")
|
|
(version "1.1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "crosstalk" version))
|
|
(sha256
|
|
(base32
|
|
"03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-lazyeval" ,r-lazyeval)
|
|
("r-r6" ,r-r6)))
|
|
(home-page "https://rstudio.github.io/crosstalk/")
|
|
(synopsis "Inter-widget interactivity for HTML widgets")
|
|
(description
|
|
"This package provides building blocks for allowing HTML widgets to
|
|
communicate with each other, with Shiny or without (i.e. static @code{.html}
|
|
files). It currently supports linked brushing and filtering.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-rook
|
|
(package
|
|
(name "r-rook")
|
|
(version "1.1-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rook" version))
|
|
(sha256
|
|
(base32
|
|
"00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
|
|
(properties `((upstream-name . "Rook")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-brew" ,r-brew)))
|
|
(home-page "https://cran.r-project.org/web/packages/Rook")
|
|
(synopsis "Web server interface for R")
|
|
(description
|
|
"This package contains the Rook specification and convenience software
|
|
for building and running Rook applications. A Rook application is an R
|
|
reference class object that implements a @code{call} method or an R closure
|
|
that takes exactly one argument, an environment, and returns a list with three
|
|
named elements: the @code{status}, the @code{headers}, and the @code{body}.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-miniui
|
|
(package
|
|
(name "r-miniui")
|
|
(version "0.1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "miniUI" version))
|
|
(sha256
|
|
(base32
|
|
"1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
|
|
(properties `((upstream-name . "miniUI")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-shiny" ,r-shiny)))
|
|
(home-page "https://cran.r-project.org/web/packages/miniUI/")
|
|
(synopsis "Shiny UI widgets for small screens")
|
|
(description
|
|
"This package provides UI widget and layout functions for writing Shiny apps that
|
|
work well on small screens.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-feather
|
|
(package
|
|
(name "r-feather")
|
|
(version "0.3.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "feather" version))
|
|
(sha256
|
|
(base32
|
|
"1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-hms" ,r-hms)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://github.com/wesm/feather")
|
|
(synopsis "R Bindings to the Feather API")
|
|
(description "Read and write feather files, a lightweight binary columnar
|
|
data store designed for maximum speed.")
|
|
(license license:asl2.0)))
|
|
|
|
(define-public r-maps
|
|
(package
|
|
(name "r-maps")
|
|
(version "3.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "maps" version))
|
|
(sha256
|
|
(base32
|
|
"05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/maps")
|
|
(synopsis "Draw geographical maps")
|
|
(description "This package provides an R module for display of maps.
|
|
Projection code and larger maps are in separate packages (@code{mapproj} and
|
|
@code{mapdata}).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-mapproj
|
|
(package
|
|
(name "r-mapproj")
|
|
(version "1.2.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mapproj" version))
|
|
(sha256
|
|
(base32
|
|
"0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-maps" ,r-maps)))
|
|
(home-page "https://cran.r-project.org/web/packages/mapproj")
|
|
(synopsis "Map projection in R")
|
|
(description "This package converts latitude/longitude into projected
|
|
coordinates.")
|
|
(license (list license:gpl2 ; The R interface
|
|
(license:non-copyleft ; The C code
|
|
"https://www.gnu.org/licenses/license-list.en.html#lucent102"
|
|
"Lucent Public License Version 1.02")))))
|
|
|
|
(define-public r-rgooglemaps
|
|
(package
|
|
(name "r-rgooglemaps")
|
|
(version "1.4.5.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RgoogleMaps" version))
|
|
(sha256
|
|
(base32
|
|
"02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
|
|
(properties `((upstream-name . "RgoogleMaps")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-png" ,r-png)
|
|
("r-sp" ,r-sp)))
|
|
(home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
|
|
(synopsis "Use Google Maps in R")
|
|
(description "This package serves two purposes:
|
|
@enumerate
|
|
@item Provide a comfortable R interface to query the Google server for static
|
|
maps, and
|
|
@item Use the map as a background image to overlay plots within R. This
|
|
requires proper coordinate scaling.
|
|
@end enumerate\n")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-geosphere
|
|
(package
|
|
(name "r-geosphere")
|
|
(version "1.5-10")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "geosphere" version))
|
|
(sha256
|
|
(base32
|
|
"15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-sp" ,r-sp)))
|
|
(home-page "https://cran.r-project.org/web/packages/geosphere")
|
|
(synopsis "Spherical trigonometry")
|
|
(description "This package computes spherical trigonometry for geographic
|
|
applications. That is, compute distances and related measures for angular
|
|
(longitude/latitude) locations.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-jpeg
|
|
(package
|
|
(name "r-jpeg")
|
|
(version "0.1-8.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "jpeg" version))
|
|
(sha256
|
|
(base32
|
|
"1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
|
|
(build-system r-build-system)
|
|
(inputs `(("libjpeg" ,libjpeg-turbo)))
|
|
(home-page "https://www.rforge.net/jpeg/")
|
|
(synopsis "Read and write JPEG images with R")
|
|
(description "This package provides a way to read, write and display
|
|
bitmap images stored in the JPEG format with R. It can read and write both
|
|
files and in-memory raw vectors.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ggmap
|
|
(package
|
|
(name "r-ggmap")
|
|
(version "3.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggmap" version))
|
|
(sha256
|
|
(base32
|
|
"13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bitops" ,r-bitops)
|
|
("r-digest" ,r-digest)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-glue" ,r-glue)
|
|
("r-httr" ,r-httr)
|
|
("r-jpeg" ,r-jpeg)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-plyr" ,r-plyr)
|
|
("r-png" ,r-png)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rgooglemaps" ,r-rgooglemaps)
|
|
("r-rjson" ,r-rjson)
|
|
("r-scales" ,r-scales)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://github.com/dkahle/ggmap")
|
|
(synopsis "Spatial visualization with ggplot2")
|
|
(description "This package provides a collection of functions to visualize
|
|
spatial data and models on top of static maps from various online sources (e.g
|
|
Google Maps and Stamen Maps). It includes tools common to those tasks,
|
|
including functions for geolocation and routing.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-haven
|
|
(package
|
|
(name "r-haven")
|
|
(version "2.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "haven" version))
|
|
(sha256
|
|
(base32
|
|
"03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(propagated-inputs
|
|
`(("r-forcats" ,r-forcats)
|
|
("r-hms" ,r-hms)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rlang" ,r-rlang)
|
|
("r-readr" ,r-readr)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyselect" ,r-tidyselect)
|
|
("r-vctrs" ,r-vctrs)))
|
|
(home-page "https://haven.tidyverse.org")
|
|
(synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
|
|
(description
|
|
"This package lets you mport foreign statistical formats into R via the
|
|
embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-amap
|
|
(package
|
|
(name "r-amap")
|
|
(version "0.8-18")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "amap" version))
|
|
(sha256
|
|
(base32
|
|
"0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
|
|
(synopsis "Another multidimensional analysis package")
|
|
(description "This package provides tools for clustering and principal
|
|
component analysis (with robust methods, and parallelized functions).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ape
|
|
(package
|
|
(name "r-ape")
|
|
(version "5.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ape" version))
|
|
(sha256
|
|
(base32
|
|
"0f74x9vx9sxpns2hlq4w2x80cd2gw42isfgncvs9pqbjf4hiyqnr"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-nlme" ,r-nlme)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "http://ape-package.ird.fr/")
|
|
(synopsis "Analyses of phylogenetics and evolution")
|
|
(description
|
|
"This package provides functions for reading, writing, plotting, and
|
|
manipulating phylogenetic trees, analyses of comparative data in a
|
|
phylogenetic framework, ancestral character analyses, analyses of
|
|
diversification and macroevolution, computing distances from DNA sequences,
|
|
and several other tools.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-abbyyr
|
|
(package
|
|
(name "r-abbyyr")
|
|
(version "0.5.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abbyyR" version))
|
|
(sha256
|
|
(base32
|
|
"1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
|
|
(properties `((upstream-name . "abbyyR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-httr" ,r-httr)
|
|
("r-plyr" ,r-plyr)
|
|
("r-progress" ,r-progress)
|
|
("r-readr" ,r-readr)
|
|
("r-xml" ,r-xml)))
|
|
(home-page "https://github.com/soodoku/abbyyR")
|
|
(synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
|
|
(description
|
|
"This package provides tools to get text from images of text using Abbyy
|
|
Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
|
|
OCR images, barcodes, forms, documents with machine readable zones, e.g.
|
|
passports and get the results in a variety of formats including plain text and
|
|
XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-colorspace
|
|
(package
|
|
(name "r-colorspace")
|
|
(version "1.4-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "colorspace" version))
|
|
(sha256
|
|
(base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/colorspace")
|
|
(synopsis "Color space manipulation")
|
|
(description
|
|
"This package carries out a mapping between assorted color spaces
|
|
including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
|
|
CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
|
|
colors are provided.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-glue
|
|
(package
|
|
(name "r-glue")
|
|
(version "1.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "glue" version))
|
|
(sha256
|
|
(base32
|
|
"1j1va4vi3g9sl0cyjdwxvh5lvh10x8k9qvnsr9zyxddcbk9qgdpq"))))
|
|
(build-system r-build-system)
|
|
;; knitr depends on glue, so we can't add knitr here to build the
|
|
;; vignettes.
|
|
#;
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/tidyverse/glue")
|
|
(synopsis "Interpreted string literals")
|
|
(description
|
|
"This package provides an implementation of interpreted string literals,
|
|
inspired by Python's Literal String Interpolation (PEP-0498) and
|
|
Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-pastecs
|
|
(package
|
|
(name "r-pastecs")
|
|
(version "1.3.21")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pastecs" version))
|
|
(sha256
|
|
(base32
|
|
"0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-boot" ,r-boot)))
|
|
(home-page "http://www.sciviews.org/pastecs")
|
|
(synopsis "Analysis of space-time ecological series")
|
|
(description
|
|
"This package provides functions for regulation, decomposition and analysis
|
|
of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
|
|
initiative to bring PASSTEC 2000 functionalities to R.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-plogr
|
|
(package
|
|
(name "r-plogr")
|
|
(version "0.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "plogr" version))
|
|
(sha256
|
|
(base32
|
|
"0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/krlmlr/plogr")
|
|
(synopsis "R bindings for the plog C++ logging library")
|
|
(description
|
|
"This package provides the header files for a stripped-down version of
|
|
the plog header-only C++ logging library, and a method to log to R's standard
|
|
error stream.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-pls
|
|
(package
|
|
(name "r-pls")
|
|
(version "2.7-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pls" version))
|
|
(sha256
|
|
(base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://mevik.net/work/software/pls.html")
|
|
(synopsis "Partial Least Squares and Principal Component Regression")
|
|
(description
|
|
"The pls package implements multivariate regression methods: Partial Least
|
|
Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
|
|
Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
|
|
|
|
@itemize
|
|
@item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
|
|
algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
|
|
@item multi-response models (or @dfn{PLS2})
|
|
@item flexible cross-validation
|
|
@item Jackknife variance estimates of regression coefficients
|
|
@item extensive and flexible plots: scores, loadings, predictions, coefficients,
|
|
(R)MSEP, R², and correlation loadings
|
|
@item formula interface, modelled after @code{lm()}, with methods for predict,
|
|
print, summary, plot, update, etc.
|
|
@item extraction functions for coefficients, scores, and loadings
|
|
@item MSEP, RMSEP, and R² estimates
|
|
@item multiplicative scatter correction (@dfn{MSC})
|
|
@end itemize\n")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ps
|
|
(package
|
|
(name "r-ps")
|
|
(version "1.3.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ps" version))
|
|
(sha256
|
|
(base32 "1x10zgvq75gnkmzqhbqn6jyvp9h1y4qxgnbdds0bwmc8ad8md903"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://ps.r-lib.org")
|
|
(synopsis "List, query, and manipulate system processes")
|
|
(description
|
|
"The ps package implements an API to list, query, and manipulate system
|
|
processes. Most of its code is based on the @code{psutil} Python package.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-pkgbuild
|
|
(package
|
|
(name "r-pkgbuild")
|
|
(version "1.0.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pkgbuild" version))
|
|
(sha256
|
|
(base32 "188r2ba7y5j80mnfqdf210af40yd28jjgx7rbya4iwcfx7rzqjdi"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-callr" ,r-callr)
|
|
("r-cli" ,r-cli)
|
|
("r-crayon" ,r-crayon)
|
|
("r-desc" ,r-desc)
|
|
("r-prettyunits" ,r-prettyunits)
|
|
("r-r6" ,r-r6)
|
|
("r-rprojroot" ,r-rprojroot)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/r-pkgs/pkgbuild")
|
|
(synopsis "Find tools needed to build R packages")
|
|
(description
|
|
"This package provides functions used to build R packages. It locates
|
|
compilers needed to build R packages on various platforms and ensures the PATH
|
|
is configured appropriately so R can use them.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-pkgload
|
|
(package
|
|
(name "r-pkgload")
|
|
(version "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pkgload" version))
|
|
(sha256
|
|
(base32
|
|
"03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cli" ,r-cli)
|
|
("r-crayon" ,r-crayon)
|
|
("r-desc" ,r-desc)
|
|
("r-pkgbuild" ,r-pkgbuild)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rprojroot" ,r-rprojroot)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/r-lib/pkgload")
|
|
(synopsis "Simulate package installation and attach")
|
|
(description
|
|
"This package simulates the process of installing a package and then
|
|
attaching it. This is a key part of the @code{devtools} package as it allows
|
|
you to rapidly iterate while developing a package.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-rcpp
|
|
(package
|
|
(name "r-rcpp")
|
|
(version "1.0.4.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rcpp" version))
|
|
(sha256
|
|
(base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.rcpp.org")
|
|
(synopsis "Seamless R and C++ integration")
|
|
(description
|
|
"The Rcpp package provides R functions as well as C++ classes which offer
|
|
a seamless integration of R and C++. Many R data types and objects can be
|
|
mapped back and forth to C++ equivalents which facilitates both writing of new
|
|
code as well as easier integration of third-party libraries. Documentation
|
|
about Rcpp is provided by several vignettes included in this package, via the
|
|
@code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
|
|
and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
|
|
@code{citation(\"Rcpp\")} for details on these last two.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-bindr
|
|
(package
|
|
(name "r-bindr")
|
|
(version "0.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bindr" version))
|
|
(sha256
|
|
(base32
|
|
"1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/krlmlr/bindr")
|
|
(synopsis "Parametrized active bindings")
|
|
(description
|
|
"This package provides a simple interface for creating active bindings
|
|
where the bound function accepts additional arguments.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-bindrcpp
|
|
(package
|
|
(name "r-bindrcpp")
|
|
(version "0.2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bindrcpp" version))
|
|
(sha256
|
|
(base32
|
|
"0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bindr" ,r-bindr)
|
|
("r-plogr" ,r-plogr)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/krlmlr/bindrcpp")
|
|
(synopsis "Rcpp interface to active bindings")
|
|
(description
|
|
"This package provides an easy way to fill an environment with active
|
|
bindings that call a C++ function.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-auc
|
|
(package
|
|
(name "r-auc")
|
|
(version "0.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "AUC" version))
|
|
(sha256
|
|
(base32
|
|
"0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
|
|
(properties `((upstream-name . "AUC")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/AUC")
|
|
(synopsis "Compute the area under the curve of selected measures")
|
|
(description
|
|
"This package includes functions to compute the area under the curve of
|
|
selected measures: the area under the sensitivity curve (AUSEC), the area
|
|
under the specificity curve (AUSPC), the area under the accuracy
|
|
curve (AUACC), and the area under the receiver operating characteristic
|
|
curve (AUROC). The curves can also be visualized. Support for partial areas
|
|
is provided.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-calibrate
|
|
(package
|
|
(name "r-calibrate")
|
|
(version "1.7.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "calibrate" version))
|
|
(sha256
|
|
(base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)))
|
|
(home-page "https://cran.r-project.org/web/packages/calibrate")
|
|
(synopsis "Calibration of scatterplot and biplot axes")
|
|
(description
|
|
"This is a package for drawing calibrated scales with tick marks
|
|
on (non-orthogonal) variable vectors in scatterplots and biplots.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-shape
|
|
(package
|
|
(name "r-shape")
|
|
(version "1.4.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shape" version))
|
|
(sha256
|
|
(base32
|
|
"0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/shape")
|
|
(synopsis "Functions for plotting graphical shapes")
|
|
(description
|
|
"This package provides functions for plotting graphical shapes such as
|
|
ellipses, circles, cylinders, arrows, ...")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-globaloptions
|
|
(package
|
|
(name "r-globaloptions")
|
|
(version "0.1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "GlobalOptions" version))
|
|
(sha256
|
|
(base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
|
|
(properties `((upstream-name . "GlobalOptions")))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/jokergoo/GlobalOptions")
|
|
(synopsis "Generate functions to get or set global options")
|
|
(description
|
|
"This package provides more controls on the option values such as
|
|
validation and filtering on the values, making options invisible or private.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-circlize
|
|
(package
|
|
(name "r-circlize")
|
|
(version "0.4.10")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "circlize" version))
|
|
(sha256
|
|
(base32
|
|
"1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-colorspace" ,r-colorspace)
|
|
("r-globaloptions" ,r-globaloptions)
|
|
("r-shape" ,r-shape)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/jokergoo/circlize")
|
|
(synopsis "Circular visualization")
|
|
(description
|
|
"Circular layout is an efficient way to visualise huge amounts of
|
|
information. This package provides an implementation of circular layout
|
|
generation in R as well as an enhancement of available software. Its
|
|
flexibility is based on the usage of low-level graphics functions such that
|
|
self-defined high-level graphics can be easily implemented by users for
|
|
specific purposes. Together with the seamless connection between the powerful
|
|
computational and visual environment in R, it gives users more convenience and
|
|
freedom to design figures for better understanding complex patterns behind
|
|
multi-dimensional data.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-powerlaw
|
|
(package
|
|
(name "r-powerlaw")
|
|
(version "0.70.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "poweRlaw" version))
|
|
(sha256
|
|
(base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
|
|
(properties `((upstream-name . "poweRlaw")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-pracma" ,r-pracma)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/csgillespie/poweRlaw")
|
|
(synopsis "Tools for the analysis of heavy tailed distributions")
|
|
(description
|
|
"This package provides an implementation of maximum likelihood estimators
|
|
for a variety of heavy tailed distributions, including both the discrete and
|
|
continuous power law distributions. Additionally, a goodness-of-fit based
|
|
approach is used to estimate the lower cut-off for the scaling region.")
|
|
;; Any of these GPL versions.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-compare
|
|
(package
|
|
(name "r-compare")
|
|
(version "0.2-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "compare" version))
|
|
(sha256
|
|
(base32
|
|
"0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/compare")
|
|
(synopsis "Comparing objects for differences")
|
|
(description
|
|
"This package provides functions to compare a model object to a
|
|
comparison object. If the objects are not identical, the functions can be
|
|
instructed to explore various modifications of the objects (e.g., sorting
|
|
rows, dropping names) to see if the modified versions are identical.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-dendextend
|
|
(package
|
|
(name "r-dendextend")
|
|
(version "1.13.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dendextend" version))
|
|
(sha256
|
|
(base32
|
|
"1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-viridis" ,r-viridis)))
|
|
(home-page "https://cran.r-project.org/web/packages/dendextend")
|
|
(synopsis "Extending 'dendrogram' functionality in R")
|
|
(description
|
|
"This package offers a set of functions for extending @code{dendrogram}
|
|
objects in R, letting you visualize and compare trees of hierarchical
|
|
clusterings. You can adjust a tree's graphical parameters (the color, size,
|
|
type, etc of its branches, nodes and labels) and visually and statistically
|
|
compare different dendrograms to one another.")
|
|
;; Any of these versions
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-getoptlong
|
|
(package
|
|
(name "r-getoptlong")
|
|
(version "1.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "GetoptLong" version))
|
|
(sha256
|
|
(base32
|
|
"1fswgy5j4xaipqs7nk7nzrl66vrchhxrk0w7hcsbyij3sxgn3z9j"))))
|
|
(properties `((upstream-name . "GetoptLong")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("perl" ,perl)))
|
|
(propagated-inputs
|
|
`(("r-crayon" ,r-crayon)
|
|
("r-globaloptions" ,r-globaloptions)
|
|
("r-rjson" ,r-rjson)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/jokergoo/GetoptLong")
|
|
(synopsis "Parsing command-line arguments and variable interpolation")
|
|
(description
|
|
"This is yet another command-line argument parser which wraps the
|
|
powerful Perl module @code{Getopt::Long} and with some adaptation for easier
|
|
use in R. It also provides a simple way for variable interpolation in R.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-fastmatch
|
|
(package
|
|
(name "r-fastmatch")
|
|
(version "1.1-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fastmatch" version))
|
|
(sha256
|
|
(base32
|
|
"0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://www.rforge.net/fastmatch")
|
|
(synopsis "Fast match function")
|
|
(description
|
|
"This package provides a fast @code{match} replacement for cases that
|
|
require repeated look-ups. It is slightly faster that R's built-in
|
|
@code{match} function on first match against a table, but extremely fast on
|
|
any subsequent lookup as it keeps the hash table in memory.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ff
|
|
(package
|
|
(name "r-ff")
|
|
(version "2.2-14.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ff" version))
|
|
(sha256
|
|
(base32
|
|
"1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-bit" ,r-bit)))
|
|
(home-page "http://ff.r-forge.r-project.org/")
|
|
(synopsis "Memory-efficient storage of large data on disk and access functions")
|
|
(description
|
|
"This package provides data structures that are stored on disk but
|
|
behave (almost) as if they were in RAM by transparently mapping only a section
|
|
in main memory.")
|
|
;; error Architecture not supported.
|
|
(supported-systems (delete "aarch64-linux" %supported-systems))
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ffbase
|
|
(package
|
|
(name "r-ffbase")
|
|
(version "0.12.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ffbase" version))
|
|
(sha256
|
|
(base32
|
|
"0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bit" ,r-bit)
|
|
("r-fastmatch" ,r-fastmatch)
|
|
("r-ff" ,r-ff)))
|
|
(home-page "http://github.com/edwindj/ffbase")
|
|
(synopsis "Basic statistical functions for package 'ff'")
|
|
(description
|
|
"This package extends the out of memory vectors of @code{ff} with
|
|
statistical functions and other utilities to ease their usage.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-prettyunits
|
|
(package
|
|
(name "r-prettyunits")
|
|
(version "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "prettyunits" version))
|
|
(sha256
|
|
(base32
|
|
"1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/gaborcsardi/prettyunits")
|
|
(synopsis "Pretty, human readable formatting of quantities")
|
|
(description
|
|
"This package provides tools for pretty, human readable formatting of
|
|
quantities.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-reshape
|
|
(package
|
|
(name "r-reshape")
|
|
(version "0.8.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "reshape" version))
|
|
(sha256
|
|
(base32
|
|
"0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-plyr" ,r-plyr)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "http://had.co.nz/reshape")
|
|
(synopsis "Flexibly reshape data")
|
|
(description
|
|
"Flexibly restructure and aggregate data using just two functions:
|
|
@code{melt} and @code{cast}. This package provides them.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-progress
|
|
(package
|
|
(name "r-progress")
|
|
(version "1.2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "progress" version))
|
|
(sha256
|
|
(base32
|
|
"0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-crayon" ,r-crayon)
|
|
("r-hms" ,r-hms)
|
|
("r-prettyunits" ,r-prettyunits)
|
|
("r-r6" ,r-r6)))
|
|
(home-page "https://github.com/gaborcsardi/progress")
|
|
(synopsis "Terminal progress bars")
|
|
(description
|
|
"This package provides configurable progress bars. They may include
|
|
percentage, elapsed time, and/or the estimated completion time. They work in
|
|
terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
|
|
package also provides a C++ API, that works with or without Rcpp.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-ggally
|
|
(package
|
|
(name "r-ggally")
|
|
(version "2.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "GGally" version))
|
|
(sha256
|
|
(base32
|
|
"1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
|
|
(properties `((upstream-name . "GGally")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("libressl" ,libressl)))
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-gtable" ,r-gtable)
|
|
("r-lifecycle" ,r-lifecycle)
|
|
("r-plyr" ,r-plyr)
|
|
("r-progress" ,r-progress)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-reshape" ,r-reshape)
|
|
("r-rlang" ,r-rlang)
|
|
("r-scales" ,r-scales)))
|
|
(home-page "https://ggobi.github.io/ggally")
|
|
(synopsis "Extension to ggplot2")
|
|
(description
|
|
"The R package ggplot2 is a plotting system based on the grammar of
|
|
graphics. GGally extends ggplot2 by adding several functions to reduce the
|
|
complexity of combining geometric objects with transformed data. Some of
|
|
these functions include a pairwise plot matrix, a two group pairwise plot
|
|
matrix, a parallel coordinates plot, a survival plot, and several functions to
|
|
plot networks.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-proxy
|
|
(package
|
|
(name "r-proxy")
|
|
(version "0.4-24")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "proxy" version))
|
|
(sha256
|
|
(base32
|
|
"0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/proxy")
|
|
(synopsis "Distance and similarity measures")
|
|
(description
|
|
"This package provides an extensible framework for the efficient
|
|
calculation of auto- and cross-proximities, along with implementations of the
|
|
most popular ones.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-sp
|
|
(package
|
|
(name "r-sp")
|
|
(version "1.4-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sp" version))
|
|
(sha256
|
|
(base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(home-page "https://cran.r-project.org/web/packages/sp")
|
|
(synopsis "Classes and methods for spatial data")
|
|
(description
|
|
"This package provides classes and methods for spatial data; the classes
|
|
document where the spatial location information resides, for 2D or 3D data.
|
|
Utility functions are provided, e.g. for plotting data as maps, spatial
|
|
selection, as well as methods for retrieving coordinates, for subsetting,
|
|
print, summary, etc.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rmtstat
|
|
(package
|
|
(name "r-rmtstat")
|
|
(version "0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RMTstat" version))
|
|
(sha256
|
|
(base32
|
|
"1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
|
|
(properties `((upstream-name . "RMTstat")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/RMTstat")
|
|
(synopsis "Distributions, statistics and tests derived from random matrix theory")
|
|
(description
|
|
"This package provides functions for working with the Tracy-Widom laws
|
|
and other distributions related to the eigenvalues of large Wishart
|
|
matrices.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-rmpi
|
|
(package
|
|
(name "r-rmpi")
|
|
(version "0.6-9")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rmpi" version))
|
|
(sha256
|
|
(base32
|
|
"1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
|
|
(properties `((upstream-name . "Rmpi")))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
|
|
#:phases (modify-phases %standard-phases
|
|
(add-before 'install 'mpi-setup
|
|
,%openmpi-setup))))
|
|
(inputs
|
|
`(("openmpi" ,openmpi)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
|
|
(synopsis "R interface to message-passing interface (MPI)")
|
|
(description
|
|
"This package provides an interface (wrapper) to MPI APIs. It also
|
|
provides an interactive R manager and worker environment.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-lmoments
|
|
(package
|
|
(name "r-lmoments")
|
|
(version "1.3-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Lmoments" version))
|
|
(sha256
|
|
(base32
|
|
"0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
|
|
(properties `((upstream-name . "Lmoments")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)))
|
|
(home-page "http://www.tilastotiede.fi/juha_karvanen.html")
|
|
(synopsis "L-moments and quantile mixtures")
|
|
(description
|
|
"This package contains functions to estimate L-moments and trimmed
|
|
L-moments from the data. It also contains functions to estimate the
|
|
parameters of the normal polynomial quantile mixture and the Cauchy polynomial
|
|
quantile mixture from L-moments and trimmed L-moments.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-distillery
|
|
(package
|
|
(name "r-distillery")
|
|
(version "1.0-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "distillery" version))
|
|
(sha256
|
|
(base32
|
|
"0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://ral.ucar.edu/staff/ericg/")
|
|
(synopsis "Functions for confidence intervals and object information")
|
|
(description
|
|
"This package provides some very simple method functions for confidence
|
|
interval calculation and to distill pertinent information from a potentially
|
|
complex object; primarily used in common with the packages extRemes and
|
|
SpatialVx.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-extremes
|
|
(package
|
|
(name "r-extremes")
|
|
(version "2.0-12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "extRemes" version))
|
|
(sha256
|
|
(base32
|
|
"0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
|
|
(properties `((upstream-name . "extRemes")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-distillery" ,r-distillery)
|
|
("r-lmoments" ,r-lmoments)))
|
|
(home-page "https://www.assessment.ucar.edu/toolkit/")
|
|
(synopsis "Extreme value analysis")
|
|
(description
|
|
"ExtRemes is a suite of functions for carrying out analyses on the
|
|
extreme values of a process of interest; be they block maxima over long blocks
|
|
or excesses over a high threshold.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-lmtest
|
|
(package
|
|
(name "r-lmtest")
|
|
(version "0.9-37")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lmtest" version))
|
|
(sha256
|
|
(base32
|
|
"02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-zoo" ,r-zoo)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/lmtest")
|
|
(synopsis "Testing linear regression models")
|
|
(description
|
|
"This package provides a collection of tests, data sets, and examples for
|
|
diagnostic checking in linear regression models. Furthermore, some generic
|
|
tools for inference in parametric models are provided.")
|
|
;; Either version is okay
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-idr
|
|
(package
|
|
(name "r-idr")
|
|
(version "1.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "idr" version))
|
|
(sha256
|
|
(base32
|
|
"05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/idr/")
|
|
(synopsis "Irreproducible discovery rate")
|
|
(description
|
|
"This is a package for estimating the copula mixture model and plotting
|
|
correspondence curves in \"Measuring reproducibility of high-throughput
|
|
experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
|
|
by Li, Brown, Huang, and Bickel")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-inline
|
|
(package
|
|
(name "r-inline")
|
|
(version "0.3.15")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "inline" version))
|
|
(sha256
|
|
(base32
|
|
"0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/inline")
|
|
(synopsis "Functions to inline C, C++, Fortran function calls from R")
|
|
(description
|
|
"This package provides functionality to dynamically define R functions
|
|
and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
|
|
@code{.Call} calling conventions.")
|
|
;; Any version of the LGPL.
|
|
(license license:lgpl3+)))
|
|
|
|
(define-public r-inum
|
|
(package
|
|
(name "r-inum")
|
|
(version "1.0-1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "inum" version))
|
|
(sha256
|
|
(base32
|
|
"16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-libcoin" ,r-libcoin)))
|
|
(home-page "https://cran.r-project.org/web/packages/inum/")
|
|
(synopsis "Interval and enum-type representation of vectors")
|
|
(description
|
|
"This package provides an enum-type representation of vectors and
|
|
representation of intervals, including a method of coercing variables
|
|
in data frames.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-bdsmatrix
|
|
(package
|
|
(name "r-bdsmatrix")
|
|
(version "1.3-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bdsmatrix" version))
|
|
(sha256
|
|
(base32
|
|
"1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
|
|
(properties `((upstream-name . "bdsmatrix")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
|
|
(synopsis "Routines for block diagonal symmetric matrices")
|
|
(description
|
|
"This package provides procedures to work with block diagonal symmetric
|
|
matrices, a special case of sparse matrices.")
|
|
(license license:lgpl2.0)))
|
|
|
|
(define-public r-bbmle
|
|
(package
|
|
(name "r-bbmle")
|
|
(version "1.0.23.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bbmle" version))
|
|
(sha256
|
|
(base32
|
|
"0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bdsmatrix" ,r-bdsmatrix)
|
|
("r-lattice" ,r-lattice)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-mvtnorm" ,r-mvtnorm)
|
|
("r-numderiv" ,r-numderiv)))
|
|
(home-page "https://cran.r-project.org/web/packages/bbmle")
|
|
(synopsis "Tools for General Maximum Likelihood Estimation")
|
|
(description
|
|
"This package provides methods and functions for fitting maximum
|
|
likelihood models in R. This package modifies and extends the @code{mle}
|
|
classes in the @code{stats4} package.")
|
|
;; Any version of the GPL
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-emdbook
|
|
(package
|
|
(name "r-emdbook")
|
|
(version "1.3.12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "emdbook" version))
|
|
(sha256
|
|
(base32
|
|
"0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bbmle" ,r-bbmle)
|
|
("r-coda" ,r-coda)
|
|
("r-lattice" ,r-lattice)
|
|
("r-mass" ,r-mass)
|
|
("r-plyr" ,r-plyr)))
|
|
(home-page "http://www.math.mcmaster.ca/bolker/emdbook")
|
|
(synopsis "Support functions and data for \"Ecological Models and Data\"")
|
|
(description
|
|
"This package provides auxiliary functions and data sets for \"Ecological
|
|
Models and Data\", a book presenting maximum likelihood estimation and related
|
|
topics for ecologists (ISBN 978-0-691-12522-0).")
|
|
;; Any GPL version
|
|
(license (l |